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Author Topic: Understanding recLOH - Palindromic mutation events  (Read 11186 times)
Terry Barton
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« on: April 26, 2007, 12:25:13 PM »

Do you have the same result at both alleles of a multi-marker (459, 464, CDY(aka 724), ...?)  You may have had a mutation event called a recLOH - Recombinational Loss of Heterozygosity

Muli-markers on the P1 Palindrome: DYF359, DYF401, DYF387, DYS459, DYF385, DYS724(CDY), DYF371, DYF408, DYF399, DYS464 & DYS725

This is a relatively new discovery - which has been spearheaded by Thomas Krahn, who started DNA Fingerprint, and then merged into FamilyTreeDNA.  The advanced tests offered by FTDNA can be helpful in evaluating this.  

As it is difficult to find a lot of info about recLOH, I have compiled the links I could find at our Reference Page:  http://worldfamilies.net/reference

To get an Advanced Test, go to your personal page at FTDNA, click on "Order Tests" in the upper right part of the page and then click on "Advanced Tests".  

Terry
« Last Edit: January 23, 2014, 10:34:50 PM by Terry Barton » Logged
Raymond Wing
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« Reply #1 on: August 28, 2008, 08:06:49 PM »

recLOH has been called (by some) to fall somewhere between STR markers and SNP markers.

What they mean by this is that the recLOH event (as a mutation) is much rarer than a mutation on a STR marker, but appears to be more common than a SNP mutation.


The end result of a recLOH event is the two two locations of a marker end up with the same value.  Over time/generations, these marker values drift away from one another (due to STR mutations) which tends to make a recLOH event appear rarer than it really is.  For instance, if your marker values for 385a & 385b are say 11 & 12, then it is quite likely somewhere in your past there was a recLOH event which created a 11,11 situation and after this recLOH there was a mutation to one of these pairs.
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cmblandford
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« Reply #2 on: October 12, 2009, 03:50:51 PM »

I appear to have several recLOH events in my 67 markers.  The most interesting is 459a=6 and 459b=9.  My brother shows exactly the same 37 DYS# I show - he has not tested to 67.  This makes it very difficult to find matches that are "old".  Although a recent match stands out very clearly.  I have a difficult time matching up to modals.  The most unusual is 459a=6 which almost no others share. 

Any comments on 459a=6?
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Y-DNA:  R-DF13*


Surname Project:  Blandford

Kit:  ft115893   Ysearch:  EYSPZ


Earliest Known Ancestor:  Thomas Blanford; Dorset, England; born 1648


Terry Barton
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« Reply #3 on: October 12, 2009, 04:52:05 PM »

As I understand it, the most important aspect is that what appears to be a lot of mutations turns out to be one single event - allowing someone who has them to understand how their much different result can be possible - and for them to  actually be genetically related as paper trails predict.

I am not one of the folks who gets excited about a particular result at a particular marker - or the approaches working on the assumptions that certain marker results are "modal" for a particular group.  Probably, a significant percentage are "modal"- but what about the 10, 20 or 30% who don't have the modal because of a "recent" mutation - or do have the modal - but have it because of a "recent" mutation. 

The 6 would be important because it is unusual.  However, if you have a 6 and a 9 at 459, I don't think that is a recLOH.  I think you simply have an unusual result at 459.

The most important question is whether or not that you have apparent matches - matches which the recLOH event may be partially masking - or confusing.  Then - you are looking to see what of the differences can be explained by recLOH.  If you can direct me to the results where you and your matches are shown online, I can see what I can infer.

These recLOH are relatively unusual - so Thomas Krahn at FTDNA may wish to take a look himself.

Terry
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ceo.peo1
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« Reply #4 on: February 04, 2010, 06:57:12 AM »

It is important to distinguish between DNA damage and mutation, the two major types of error in DNA. DNA damages and mutation are fundamentally different. Damages are physical abnormalities in the DNA, such as single and double strand breaks, 8-hydroxydeoxyguanosine residues and polycyclic aromatic hydrocarbon adducts. DNA damages can be recognized by enzymes, and thus they can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. If a cell retains DNA damage, transcription of a gene can be prevented and thus translation into a protein will also be blocked. Replication may also be blocked and/or the cell may die.



________________________________________
70-293 ll 70-620 ll 70-640
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J F Chambers
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« Reply #5 on: August 20, 2010, 03:54:34 PM »

My husband has same numbers at 459a/b 8, 464a/b 14, 464c/d 17, CDYa/b 32. We need to know which test of the advanced tests on FTDNA to choose. Will appreciate your help.
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Terry Barton
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« Reply #6 on: August 24, 2010, 08:53:50 PM »

The first thing I would do is to compare within the Chambers project and see if there are folks that you match except on these palindromes.  If so - they are most likely your genetic kin

What do you want to accomplish with another test?  There is an advanced test at FTDNA for the palindromic markers - but I am not sure what good it would do for you to get it.

Terry
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JohnnieRayK
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« Reply #7 on: February 20, 2013, 04:29:30 PM »

HELP!  I need someone to explain something to me.

I recently had a Y-DNA test run at FamilyTreeDNA.com The results are puzzling for marker 385a/385b in the Kirkpatrick Family. The Max count for the expected group is 18/18, minimum of 16/17 and mode of 17/18. The results from my test was 11/17, a mutation of -6 for 385a. I asked FTDNA to recheck the reults as they seem WAY out of line. After 7 weeks of no answers, I re-emailed them and got the following reply:

---------------------------------------------------------

Thanks for your patience. I have heart back from our Y-DNA scientist in the lab regarding your question. Here is the official conclusion:

The value is correct, and your DYS385 (a/b) result is indeed 11-17. She has stated that the others have 17-17 most likely because they probably had a recLOH event (recombinational loss of heterozygosity) in their family. They lost the short value (11 or maybe 12) which got replaced by a 2nd value of 17. Males with 16-17 or 17-18 results had a recLOH event first and then one of their 17s mutated up or down. This all might happen many generations ago.

I hope this helps!

---------------------------------------------------

Does this mean that my value of 11 puts our line closer to the progenitor of this family group?

If someone could explain IN ENGLISH, or simpler terms, I'd be ever so grateful.

Thanks,

Tom
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Terry Barton
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« Reply #8 on: February 20, 2013, 04:46:13 PM »

I would interpret this the same as you - that the 11-17 is more like the progenitor and the men with a 17-17 have the recLOH in their branch.

Assuming that you don't have a back mutation (I've never seen a discussion about back-mutations and recLOH together) - the men with the 17-17 are descended from a more recent common ancestor than you share with them. 

A 16-17 would presumably be a single step mutation away from 17-17.    The more traditional mutation is a 16-16 or 18-18 - also considered to be one mutation

The other possibility is that you did have a six step mutation.  We have a man with an 8 step mutation at 557!   
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Erik Maher
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« Reply #9 on: July 18, 2013, 08:15:56 PM »

I've started a new FTDNA project looking into the DF13+ 9919 clusters and into recLOHs in general.
www.ftdna.com/public/recloh
I'm in the process of rewriting the Background page so that the recLOH information will be more accurate and easier to understand.

Putting accurate information on the project is of great importance (not to send anyone astray with false information), so with that in mind, I have a question regarding recLOHs:

Can the two-part 389 marker ever be a recLOH?  I'm 99% sure that the answer is no, as Thomas Krahn does not show 389 as being part of the palindromic region:
http://www.dna-fingerprint.com/static/PalindromicRegion-V2.pdf
My understanding is that recLOHs can only occur on multicopy markers existing in the palindromic region, and 389 is the one "multicopy" (dashed) marker that is NOT in the palindromic region.

Furthermore, I've never seen 389i and 389ii in a doubled combination (say, 389i=14, 389ii=28) with other markers (such as 385=11-11 or 459=9-9) that would suggest its involvement in a recLOH event.  I just wanted to be 100% sure.  Let's say, for example, that a person has one of these combinations of 389 values:

389i=12 and 389ii=24,
or
389i=13 and 389ii=26,
or
389i=14 and 389ii=28,
or
389i=15 and 389ii=30,
or
389i=16 and 389ii=32

In these examples, 389, a multicopy marker, is readable in the forward direction as one value, and in the reverse direction as the other value.  This apparent doubling in the examples above has nothing whatsoever to do with recLOHs, correct?  This is a so-called "multicopy" marker whose two "copies" are actually different readings of the same marker - one reading a subset of the other, producing two alleles - rather than a true "multicopy" marker with two separate chunks of DNA producing the two different alleles.  Am I understanding this correctly?

Thanks in advance.
Erik.
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Terry Barton
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« Reply #10 on: July 18, 2013, 08:36:47 PM »

Fantastic!  I have been wanting an easy to understand explanation of recLOH that I can  refer folks to.  

As far as 389, I am with you, nearly - but not quite - certain that 389 does not participate in the recLOH event.

For those who don't understand how 389 is reported:

FTDNA (and others) report the first part of 389 as the first allele and the second part as the sum of the two alleles.  (I don't understand why.  It makes it much harder to work with!)  In your example: 14-28 - that is how FTDNA would report it.

However, National Geographic uses a different convention and reports it as 14-14.  (So - as you recognize in your posting - it can actually be viewed as a double when reporting with the convention used by NGGP.)

I wish everyone used the convention that NGGP uses, as it is much easier when counting mutations!

Terry
« Last Edit: July 18, 2013, 08:41:05 PM by Terry Barton » Logged
Alpine
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« Reply #11 on: October 11, 2013, 02:40:29 AM »

I know about the Kittler tests, but I am DYS385 = 13,13
does this DYS385 indicate anything in the way of age of lineage or origins , something like what DYS390 shows?
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YDna = T1a2b (L446)
MtDNA = H2a1c (haplofind)

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